TY - JOUR
T1 - Identifying sequence features that drive ribosomal association for lncRNA 06 Biological Sciences 0604 Genetics
AU - Zeng, Chao
AU - Hamada, Michiaki
N1 - Funding Information:
Publication costs are funded by Waseda University [basic research budget]. This work was suppoted by the Ministry of Education, Culture, Sports, Science and Technology (KAKENHI) [grant numbers JP17K20032, JP16H05879, JP16H01318, and JP16H02484 to MH].
Publisher Copyright:
© 2018 The Author(s).
PY - 2018/12/31
Y1 - 2018/12/31
N2 - Background: With the increasing number of annotated long noncoding RNAs (lncRNAs) from the genome, researchers are continually updating their understanding of lncRNAs. Recently, thousands of lncRNAs have been reported to be associated with ribosomes in mammals. However, their biological functions or mechanisms are still unclear. Results: In this study, we tried to investigate the sequence features involved in the ribosomal association of lncRNA. We have extracted ninety-nine sequence features corresponding to different biological mechanisms (i.e., RNA splicing, putative ORF, k-mer frequency, RNA modification, RNA secondary structure, and repeat element). An 1 regularized logistic regression model was applied to screen these features. Finally, we obtained fifteen and nine important features for the ribosomal association of human and mouse lncRNAs, respectively. Conclusion: To our knowledge, this is the first study to characterize ribosome-associated lncRNAs and ribosome-free lncRNAs from the perspective of sequence features. These sequence features that were identified in this study may shed light on the biological mechanism of the ribosomal association and provide important clues for functional analysis of lncRNAs.
AB - Background: With the increasing number of annotated long noncoding RNAs (lncRNAs) from the genome, researchers are continually updating their understanding of lncRNAs. Recently, thousands of lncRNAs have been reported to be associated with ribosomes in mammals. However, their biological functions or mechanisms are still unclear. Results: In this study, we tried to investigate the sequence features involved in the ribosomal association of lncRNA. We have extracted ninety-nine sequence features corresponding to different biological mechanisms (i.e., RNA splicing, putative ORF, k-mer frequency, RNA modification, RNA secondary structure, and repeat element). An 1 regularized logistic regression model was applied to screen these features. Finally, we obtained fifteen and nine important features for the ribosomal association of human and mouse lncRNAs, respectively. Conclusion: To our knowledge, this is the first study to characterize ribosome-associated lncRNAs and ribosome-free lncRNAs from the perspective of sequence features. These sequence features that were identified in this study may shed light on the biological mechanism of the ribosomal association and provide important clues for functional analysis of lncRNAs.
KW - Feature selection
KW - Ribosome-associated
KW - Sequence feature
KW - lncRNA
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U2 - 10.1186/s12864-018-5275-8
DO - 10.1186/s12864-018-5275-8
M3 - Article
C2 - 30598103
AN - SCOPUS:85059252859
SN - 1471-2164
VL - 19
JO - BMC Genomics
JF - BMC Genomics
M1 - 906
ER -